A former hedge fund portfolio manager charged with carrying out a record-setting insider trading scheme pleaded not guilty to insider trading charges Thursday as the prosecution hinted that he would not be the last person arrested in the case.

Mathew Martoma, 38, of Boca Raton, Fla., persuaded a medical professor to leak secret data from an Alzheimer’s disease drug trial between 2006 and 2008 when Martoma did work for an expert consulting service in New York, prosecutors said. The government said inside information Martoma learned about the joint drug trial by pharmaceutical companies Elan Corp. and Wyeth enabled other investment professionals to make a quarter of a billion dollars illegally.

Martoma, who is accused of earning $9 million in bonuses for the year when the trades were made, entered his plea in U.S. District Court in Manhattan to charges of conspiracy and securities fraud. He remained free on bail.

He said three times: “I plead not guilty, your honor” as Judge Paul G. Gardephe read the charges, a single count of conspiracy and two counts of securities fraud. Arrested in November, Martoma arrived in court hand-in-hand with his wife. His parents sat among court spectators.

Assistant U.S. Attorney Arlo Devlin-Brown said the government would rely heavily at trial on trading and phone records as well as emails and other documents. He said most of the evidence would be turned over to the defense lawyers by mid-January, but he left open the possibility that other evidence will be produced later.

“There’s an ongoing investigation in this and related matters,” he said.

The arrest of Martoma has increased speculation that the government is taking a hard look at the practices of billionaire hedge fund owner Steven A. Cohen. Martoma worked for an affiliate of Cohen’s Stamford, Conn.-based firm, SAC Capital Advisors.

In court papers, it has been widely assumed that Cohen is the unidentified “Hedge Fund Owner” repeatedly referenced in a criminal complaint against Martoma. The papers make it appear that Cohen rejected the advice of his own analysts and instead bet heavily on Martoma’s tips about secret data from a study of the experimental Alzheimer’s drug.

An SAC spokesman has said the company and Cohen are cooperating with the inquiry and “are confident that they have acted appropriately.”